diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 37a5da0d41..c4f9bf6aff 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1135,7 +1135,7 @@ VORONOI package ----------------------------- To build with this package, you must download and build the -`Voro++ library `_ or install a +`Voro++ library `_ or install a binary package provided by your operating system. .. tabs:: diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index c726d37ea6..33ba5937c7 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -48,9 +48,9 @@ Build using GNU make The LAMMPS manual is written in `reStructuredText `_ format which can be translated to different output format using the `Sphinx -`_ document generator tool. It also +`_ document generator tool. It also incorporates programmer documentation extracted from the LAMMPS C++ -sources through the `Doxygen `_ program. Currently +sources through the `Doxygen `_ program. Currently the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle readers) are supported. For that to work a Python 3 interpreter, the ``doxygen`` tools and internet access to diff --git a/doc/src/Developer_comm_ops.rst b/doc/src/Developer_comm_ops.rst index de09cbb260..f8444d2993 100644 --- a/doc/src/Developer_comm_ops.rst +++ b/doc/src/Developer_comm_ops.rst @@ -77,7 +77,7 @@ buffer, and they will be communicated together to minimize communication overhead. The communication buffers are defined vectors containing ``double`` values. To correctly store integers that may be 64-bit (bigint, tagint, imageint) in the buffer, you need to use the -`ubuf union `_ construct. +`ubuf union `_ construct. The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind of forward and reverse communication operations using the same *Comm* diff --git a/doc/src/Errors_debug.rst b/doc/src/Errors_debug.rst index ad0e5404e5..b3f618dbf7 100644 --- a/doc/src/Errors_debug.rst +++ b/doc/src/Errors_debug.rst @@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace There are two options to use the GDB debugger for identifying the origin of the segmentation fault or similar crash. The GDB debugger has many more features and options, as can be seen for example its `online -documentation `_. +documentation `_. Run LAMMPS from within the debugger ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst index b195721598..92a42997b8 100644 --- a/doc/src/Fortran.rst +++ b/doc/src/Fortran.rst @@ -2155,7 +2155,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type The LAMMPS :doc:`dump style movie ` supports generating movies from images on-the-fly via creating a pipe to the - `ffmpeg `_ program. + `ffmpeg `_ program. This function checks whether this feature was :ref:`enabled at compile time `. It does **not** check whether the ``ffmpeg`` itself is installed and usable. diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index b11477689b..b6d3ced0a5 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -163,10 +163,10 @@ changed. How to do this depends on the build system you are using. .. admonition:: Git protocols :class: note - The servers at github.com support the "https://" access protocol for + The servers at github.com support the "https" access protocol for anonymous, read-only access. If you have a suitably configured GitHub account, you may also use SSH protocol with the URL - "git@github.com:lammps/lammps.git". + ``git@github.com:lammps/lammps.git``. The LAMMPS GitHub project is currently overseen by Axel Kohlmeyer (Temple U, akohlmey at gmail.com). diff --git a/doc/src/Intro_citing.rst b/doc/src/Intro_citing.rst index 8a6cfde878..69ccab6162 100644 --- a/doc/src/Intro_citing.rst +++ b/doc/src/Intro_citing.rst @@ -46,7 +46,7 @@ In addition there are DOIs generated for individual stable releases: - 3 March 2020 version: `DOI:10.5281/zenodo.3726417 `_ - 29 October 2020 version: `DOI:10.5281/zenodo.4157471 `_ -- 29 September 2021 version: `DOI:10.5281/zenodo.6386596 `_ +- 29 September 2021 version: `DOI:10.5281/zenodo.6386596 `_ Home page ^^^^^^^^^ diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index 65889efd2e..3289b838d6 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks: a true molecular builder that will generate complex molecular models. See the :doc:`Tools ` page for details on tools packaged with LAMMPS. The `Pre-/post-processing page - `_ of the LAMMPS homepage + `_ of the LAMMPS homepage describes a variety of third party tools for this task. Furthermore, some internal LAMMPS commands allow reconstructing, or selectively adding topology information, as well as provide the option to insert molecule @@ -66,10 +66,9 @@ Here are suggestions on how to perform these tasks: these various options. * **Visualization:** LAMMPS can produce NETPBM, JPG, or PNG format snapshot images on-the-fly via its :doc:`dump image ` - command and pass them to an external program, `FFmpeg - `_, to generate movies from them. For - high-quality, interactive visualization, there are many excellent and - free tools available. See the `Visualization Tools + command and pass them to an external program, `FFmpeg `_, + to generate movies from them. For high-quality, interactive visualization, + there are many excellent and free tools available. See the `Visualization Tools `_ page of the LAMMPS website for visualization packages that can process LAMMPS output data. * **Plotting:** See the next bullet about Pizza.py as well as the diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index f6b0cba6e0..bc0406ee92 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -15,9 +15,6 @@ Two components are necessary for Python to be able to invoke LAMMPS code: ``liblammps.dll``) from the folder where you compiled LAMMPS. .. _ctypes: https://docs.python.org/3/library/ctypes.html -.. _python_virtualenv: https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/#creating-a-virtual-environment -.. _python_venv: https://docs.python.org/3/library/venv.html -.. _python_pep405: https://www.python.org/dev/peps/pep-0405 .. _python_install_guides: @@ -232,11 +229,11 @@ folder that the dynamic loader searches or inside of the installed install (newer/different) versions of Python packages that would potentially conflict with already installed system packages. It also does not requite any superuser privileges. See `PEP 405: - Python Virtual Environments `_ for more + Python Virtual Environments `_ for more information. To create a virtual environment in the folder ``$HOME/myenv``, - use the `venv `_ module as follows. + use the `venv `_ module as follows. .. code-block:: bash @@ -244,8 +241,9 @@ folder that the dynamic loader searches or inside of the installed python3 -m venv $HOME/myenv For Python versions prior 3.3 you can use `virtualenv - `_ command instead of "python3 -m venv". This - step has to be done only once. + `_ + command instead of "python3 -m venv". This step has to be done + only once. To activate the virtual environment type: @@ -414,10 +412,8 @@ follows: sudo pip install mpi4py -.. _mpi4py_install: https://mpi4py.readthedocs.io/en/stable/install.html - For more detailed installation instructions and additional options, -please see the `mpi4py installation `_ page. +please see the `mpi4py installation `_ page. To use ``mpi4py`` and LAMMPS in parallel from Python, you **must** make diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index fbe5a011dd..dd3354faaa 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -218,13 +218,13 @@ is used. .. _png_format: https://en.wikipedia.org/wiki/Portable_Network_Graphics .. _ppm_format: https://en.wikipedia.org/wiki/Netpbm -Similarly, the format of the resulting movie is chosen with the -*movie* dump style. This is handled by the underlying FFmpeg converter -and thus details have to be looked up in the `FFmpeg documentation -`_. Typical examples are: .avi, .mpg, -.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie -compression like *bitrate* and *framerate* can be set using the -dump_modify command as described below. +Similarly, the format of the resulting movie is chosen with the *movie* +dump style. This is handled by the underlying FFmpeg converter and thus +details have to be looked up in the `FFmpeg documentation +`_. Typical examples are: .avi, .mpg, .m4v, .mp4, +.mkv, .flv, .mov, .gif Additional settings of the movie compression like +*bitrate* and *framerate* can be set using the dump_modify command as +described below. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images @@ -651,7 +651,7 @@ MPEG or other movie file you can use: cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi Front ends for FFmpeg exist for multiple platforms. For more - information see the `FFmpeg homepage `_ + information see the `FFmpeg homepage `_ ---------- diff --git a/doc/src/group.rst b/doc/src/group.rst index 387f84921d..fb1e0fb157 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -304,7 +304,7 @@ group and running further. not all allow for use of a dynamic group. If you get an error message that this is not allowed, but feel that it should be for the fix or compute in question, then please post your reasoning to the - `LAMMPS forum at MatSci `_ + `LAMMPS forum at MatSci `_ and we can look into changing it. The same applies if you come across inconsistent behavior when dynamic groups are allowed.